Shows protein sequences as helices
emboss
emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic
$amphipathic -steps $steps -turns $turns -wheel $wheel -auto
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html